# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: pfam_list/DNA_methylase.hmm.txt # target sequence database: proteomes/Macaca_mulatta.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: DNA_methylase [M=335] Accession: PF00145.17 Description: C-5 cytosine-specific DNA methylase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-49 167.1 0.7 5.1e-47 161.1 0.0 3.0 2 tr|F7GPW3|F7GPW3_MACMU DNA (cytosine-5)-methyltransferase OS 2.2e-16 60.3 0.3 1.7e-11 44.3 0.0 2.8 3 tr|G7N534|G7N534_MACMU DNA (Cytosine-5)-methyltransferase 3B 4.8e-16 59.3 0.0 1e-11 45.0 0.0 2.3 2 tr|F7FME0|F7FME0_MACMU DNA methyltransferase 3 alpha OS=Maca 0.00075 19.2 0.0 0.0015 18.2 0.0 1.4 1 tr|F6V6X0|F6V6X0_MACMU Methyltransferase like 5 OS=Macaca mu ------ inclusion threshold ------ 0.018 14.7 1.9 0.022 14.3 1.9 1.2 1 tr|F7GPV1|F7GPV1_MACMU BCL2 interacting protein 1 OS=Macaca 0.23 11.0 7.6 0.87 9.1 7.6 2.1 1 tr|F7EXK6|F7EXK6_MACMU EF-hand calcium binding domain 12 OS= 0.26 10.9 0.0 0.4 10.2 0.0 1.3 1 tr|F6YP41|F6YP41_MACMU tRNA methyltransferase 12 homolog OS= Domain annotation for each sequence (and alignments): >> tr|F7GPW3|F7GPW3_MACMU DNA (cytosine-5)-methyltransferase OS=Macaca mulatta OX=9544 GN=DNMT1 PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -8.2 11.3 7 2.1e+04 183 293 .. 216 344 .. 146 363 .. 0.43 2 ! 161.1 0.0 1.7e-50 5.1e-47 2 334 .. 1153 1609 .. 1152 1610 .. 0.75 Alignments for each domain: == domain 1 score: -8.2 bits; conditional E-value: 7 G.........TSGGGTTS-EE.....BTTTB--GGGSSSTT-EE--.......S---HHHTS--...................B--T CS DNA_methylase 183 d....leasktlrdlleekse.....ldeektalsdklvekeekikkttkaseegypkelsrnr...................idkv 241 + +++ + r l+ e+ e + +ek++ d+ ek ++++++ +++++ ++ + tr|F7GPW3|F7GPW3_MACMU 216 KrrrvTSKERVARPLPAEEPErakpgTRSEKEEERDEKEEKRLRSQTKEPTPKQKLKE-----EpdrevragvhadededgdeK--- 294 1333222222222222222222212212222222222222222222222222222222.....122222444443333333322... PP TS...-B----S-STT-................-B-TTS---EEEETTEEE--T.TTGGG--B-BHHH CS DNA_methylase 242 eelkglsatrrksgrge................klekelaeagklqknkerfkpviekkriRrLtprE 293 + + eke +a++ +++++ ++++ R+ tp+E tr|F7GPW3|F7GPW3_MACMU 295 ----------------DekqhrsqpkdlaakrrPEEKEPEKANPQISDEKDE--DEKEEKRRKTTPKE 344 ................022222222222233322223333333333333322..34666667777666 PP == domain 2 score: 161.1 bits; conditional E-value: 1.7e-50 EEEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-............GS--...-SEEEE-- CS DNA_methylase 2 kfidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk..kvsigDitkidkk............klpe..diDlLvgGf 69 +++d f+G+GG++ g+++ag ++ +a+e+++ aa+ ++ n++ v ++D + + k lp+ d+++L+gG+ tr|F7GPW3|F7GPW3_MACMU 1153 RTLDVFSGCGGLSEGFHQAGiSDTLWAIEMWDPAAQAFRLNNPgsTVFTEDCNILLKLvmagettnsrgqRLPQkgDVEMLCGGP 1237 789*****************999*********************745555555555446666777777779998667******** PP -GGGTECTSE..E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB- CS DNA_methylase 70 PCqpfSvaGk..qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnasdyGvpQn 152 PCq+fS ++ + +++L + + + + ++P +fllENV++ ++ +++ +lk l l +GY++++ +l+a +yGv+Q tr|F7GPW3|F7GPW3_MACMU 1238 PCQGFSGMNRfnSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQT 1322 ******887654666677777**************************************************************** PP -EEEEEEEEEGGG---...............-------SS---GGG..............TSGGGTTS-EEBTTTB--GGGSSST CS DNA_methylase 153 ReRvfivgirkdleln...............vlvkvkefrfpkkkd.........leasktlrdlleekseldeektalsdklve 213 R+R +i++ +++l ++v v +++f ++ ++++t+ dl+e + + + + ++ tr|F7GPW3|F7GPW3_MACMU 1323 RRRAIILAAAPGEKLPlfpeplhvfapracqLSVVVDDKKFVSNITrlssgpfrtITVRDTMSDLPEVR-----NGASALEISYN 1402 ***********9988888888877777776633333344443333356667655555555666665543.....22222222333 PP T-EE--.......S---HHHTS--.................................B--TTS...-B----S-STT-....... CS DNA_methylase 214 keekikkttkaseegypkelsrnr.................................idkveelkglsatrrksgrge....... 258 e +++ +++ + +y+ + r+ + ++ ++++l+ t+++ ++g+ tr|F7GPW3|F7GPW3_MACMU 1403 GEPQSWFQRQLRGAQYQ-PILRDHickdmsalvaarmrhiplapgsdwrdlpnievrLSDGTMARKLRYTHHDRKNGRsssgalr 1486 33333333333333444.2222223444466667778899999999999999998884444444555555554444445566678 PP ...................................................-B-TTS---EEEETTEEE--T.TTGGG--B-BHH CS DNA_methylase 259 ...................................................klekelaeagklqknkerfkpviekkriRrLtpr 292 ++ +++ ++++k+++ v++++++R ++r tr|F7GPW3|F7GPW3_MACMU 1487 gvcscveggasgkacdpaarqfntlipwclphtgnrhnhwaglygrlewdgFFSTTVTNPEPMGKQGR----VLHPEQHRVVSVR 1567 88888888888888888888777777777777777777777777766666555666666666666666....9************ PP HHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHHH CS DNA_methylase 293 EaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakeik 334 E+ar qGfPd++ + ++ ++ +q+Gn+Vp+p+++ai+ eik tr|F7GPW3|F7GPW3_MACMU 1568 ECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIK 1609 *************************************99986 PP >> tr|G7N534|G7N534_MACMU DNA (Cytosine-5)-methyltransferase 3B OS=Macaca mulatta OX=9544 GN=DNMT3B PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.0 0.1 0.35 1.1e+03 219 275 .. 349 404 .. 306 428 .. 0.73 2 ! 44.3 0.0 5.7e-15 1.7e-11 1 120 [. 575 708 .. 575 725 .. 0.84 3 ! 12.9 0.0 2e-05 0.061 258 331 .. 769 844 .. 727 848 .. 0.77 Alignments for each domain: == domain 1 score: -1.0 bits; conditional E-value: 0.35 -.......S---HHHTS--B--TTS...-B----S-STT--B-TTS---EEEETTEE CS DNA_methylase 219 kkttkaseegypkelsrnridkveelkglsatrrksgrgeklekelaeagklqknke 275 k++++++ + + ++ r +k e+ k++++trr++ ++ ++++ ++ +l n + tr|G7N534|G7N534_MACMU 349 KPNNTQPVVNKS-KVRRAGSRKLESRKYENKTRRRTADDSATSDYCPAPKRLKTNCY 404 455555555566.67777789999999999999999988766666666555555544 PP == domain 2 score: 44.3 bits; conditional E-value: 5.7e-15 -EEEEES-TT-HHHHHHHHTT..-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-GS--...-SEEEE---GGGTECTS.EE CS DNA_methylase 1 lkfidLfaGiGGfrlgleaag..fecvaaseidkkaaktYeanfk..kvsigDitkidkkklpe.d.iDlLvgGfPCqpfSvaG.kq 80 +++++Lf+Gi l l++ g + ++ase ++ +++ +++ + +D+++i+kk+++e +Dl++gG PC++ S ++ tr|G7N534|G7N534_MACMU 575 IRVLSLFDGIATGYLVLKELGikVGKYVASEVCEESIAVGTVKHEgnIKYVNDVRNITKKNIEEwGpFDLVIGGSPCNDLSNVNpAR 661 5899*****************887778999999997777777776669999*********9998647**************87626* PP --TTSGGGHHHHHHHHHHHHH-.......-SEEEEEEEGGGGGGCCS CS DNA_methylase 81 kgfedtrgtLffeiiriikekk.......PkvfllENVkgLlkhdkg 120 kg + g Lffe+ +++ + P + ++ENV ++ dk+ tr|G7N534|G7N534_MACMU 662 KGLYEGTGRLFFEFYHLLNYSRpkegddrPFFWMFENVVAMKVGDKR 708 *******************9995555555668899999988776665 PP == domain 3 score: 12.9 bits; conditional E-value: 2e-05 --B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHHH CS DNA_methylase 258 eklekelaeagklqknkerfkpviekkriRrLtprEaarlqGfPddfefgskks..aaykqiGnsVpvpvieaiak 331 +k+++ ++++++ + k++ pv+ + ++ L E+ r+ GfP ++ s+ a+ k++G s +vpvi++++ tr|G7N534|G7N534_MACMU 769 KKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGrgARQKLLGRSWSVPVIRHLFA 844 25556666666666666666679999*********************999888888*****************986 PP >> tr|F7FME0|F7FME0_MACMU DNA methyltransferase 3 alpha OS=Macaca mulatta OX=9544 GN=DNMT3A PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 45.0 0.0 3.5e-15 1e-11 1 120 [. 634 767 .. 634 776 .. 0.88 2 ! 12.0 0.0 3.7e-05 0.11 262 332 .. 832 904 .. 784 907 .. 0.76 Alignments for each domain: == domain 1 score: 45.0 bits; conditional E-value: 3.5e-15 -EEEEES-TT-HHHHHHHHTT..-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-GS--...-SEEEE---GGGTECTS.EE CS DNA_methylase 1 lkfidLfaGiGGfrlgleaag..fecvaaseidkkaaktYeanfk..kvsigDitkidkkklpe.d.iDlLvgGfPCqpfSvaG.kq 80 +++++Lf+Gi l l+ g ++ ++ase ++ +++ +++ + gD++ +++k ++e +Dl++gG PC++ S+ ++ tr|F7FME0|F7FME0_MACMU 634 IRVLSLFDGIATGLLVLKDLGiqVDRYIASEVCEDSITVGMVRHQgkIMYVGDVRSVTQKHIQEwGpFDLVIGGSPCNDLSIVNpAR 720 5899*****************99999*********999999999988999**********9998647**************98736* PP --TTSGGGHHHHHHHHHHHHH-.......-SEEEEEEEGGGGGGCCS CS DNA_methylase 81 kgfedtrgtLffeiiriikekk.......PkvfllENVkgLlkhdkg 120 kg + g Lffe+ r++ + + P + l+ENV + +dk+ tr|F7FME0|F7FME0_MACMU 721 KGLYEGTGRLFFEFYRLLHDARpkegddrPFFWLFENVVAMGVSDKR 767 ********************995555555568899999888776664 PP == domain 2 score: 12.0 bits; conditional E-value: 3.7e-05 TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHHHH CS DNA_methylase 262 kelaeagklqknkerfkpviekkriRrLtprEaarlqGfPddfefgskks..aaykqiGnsVpvpvieaiake 332 + ++++++ + k + pv ++++ L E+ r+ GfP ++ s+ s a+ +++G s +vpvi++++ tr|F7FME0|F7FME0_MACMU 832 TITTRSNSIKQGKDQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSrlARQRLLGRSWSVPVIRHLFAP 904 33333333333333334588899999999***************999999889999*************9875 PP >> tr|F6V6X0|F6V6X0_MACMU Methyltransferase like 5 OS=Macaca mulatta OX=9544 GN=METTL5 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 18.2 0.0 5e-07 0.0015 3 70 .. 55 128 .. 54 129 .. 0.84 Alignments for each domain: == domain 1 score: 18.2 bits; conditional E-value: 5e-07 EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTTS-......GS--.-SEEEE--- CS DNA_methylase 3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigDitkidkk......klpediDlLvgGfP 70 + dL +G+G +++g ++ g ++ +id++a +++++n ++ ++ +i+ ++ + +++++D ++ +P tr|F6V6X0|F6V6X0_MACMU 55 IADLGCGCGVLSIGTAMLGAGLCVGFDIDEDALEIFNRNVEEFELTNIDMVQCDvcllsnRMSKSFDTVIMNPP 128 579**************************************888888888777666666666656777776665 PP >> tr|F7GPV1|F7GPV1_MACMU BCL2 interacting protein 1 OS=Macaca mulatta OX=9544 GN=BNIP1 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 14.3 1.9 7.4e-06 0.022 151 291 .. 53 228 .. 9 234 .. 0.67 Alignments for each domain: == domain 1 score: 14.3 bits; conditional E-value: 7.4e-06 B--EEEEEEEEEGGG---...-------SS---GGG.....TSGGGTTS-EE...BTTTB--GGGSSSTT-EE--.......S---H CS DNA_methylase 151 QnReRvfivgirkdleln...vlvkvkefrfpkkkdleasktlrdlleekse...ldeektalsdklvekeekikkttkaseegypk 231 Q R+R+ v ++ l+++ ++++ +f++p+ dle+ +d ++ e l +e +++++++++++ +++k++ +++ ++++ tr|F7GPV1|F7GPV1_MACMU 53 QLRHRIQPVLYQR-LTYSltdFSSTQHDFNSPTIPDLEQLAKEQDKES---EkqlLLQEVENHKKQMLSNQTSWRKANLTCKIAIDN 135 8899999999977.4444444455555555555544333333333333...145699999999999999999999999999999996 PP ..........HHTS--...............B--TTS...-B----S-STT-.....................-B-TTS---EEEET CS DNA_methylase 232 ..........elsrnr...............idkveelkglsatrrksgrge.....................klekelaeagklqk 272 + ++ ++ + + + tr|F7GPV1|F7GPV1_MACMU 136 lekaellqggD----LlrqrkttkeslaqtsS-------------------TiteslmgisrmmaqqvqqseeAMQSLVTSSRTILD 199 55443333332....03333444444433331...................022233333444444444455566666666666667 PP TEEE--T...........TTGGG--B-BH CS DNA_methylase 273 nkerfkp..........viekkriRrLtp 291 +e+fk+ +i+k++ R+Lt tr|F7GPV1|F7GPV1_MACMU 200 ANEEFKSmsgtiqlgrkLITKYNRRELTD 228 77777779999999999999999999986 PP >> tr|F7EXK6|F7EXK6_MACMU EF-hand calcium binding domain 12 OS=Macaca mulatta OX=9544 GN=EFCAB12 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 9.1 7.6 0.00029 0.87 143 259 .. 46 171 .. 40 506 .. 0.80 Alignments for each domain: == domain 1 score: 9.1 bits; conditional E-value: 0.00029 EGGGTT-SB--EEEEEEEEEGGG----------SS---GGG......TSGGGTTS-EEBTTTB--GGGSSSTT-EE--.......S- CS DNA_methylase 143 nasdyGvpQnReRvfivgirkdlelnvlvkvkefrfpkkkd.leasktlrdlleekseldeektalsdklvekeekikkttkaseeg 228 + +d+ pQ R+R+++v ++d++ ++++ ++ + p + + + + +d++e++ d + + ++ + +e ++ k+++e+ tr|F7EXK6|F7EXK6_MACMU 46 KQKDFRLPQTRRRIIMVPRKEDQT--PINPASQPQAPPEPIpSFKALEAKDIQEQP--EDRKTWLSRRAKLRQELESFGDVKRWLEN 128 5689******************97..455555555555432344455556666665..44555555555555555555666677777 PP --H..........HHTS--B--TTS...-B----S-STT-....- CS DNA_methylase 229 ypk..........elsrnridkveelkglsatrrksgrge....k 259 p+ +++++ +++ ++ + +t rk+g + tr|F7EXK6|F7EXK6_MACMU 129 KPSitpseakvlhMIHEEQSVQTNASQATTRTTRKKG--PrlsrQ 171 7754444444443333333333333333333333333..123341 PP >> tr|F6YP41|F6YP41_MACMU tRNA methyltransferase 12 homolog OS=Macaca mulatta OX=9544 GN=TRMT12 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.2 0.0 0.00013 0.4 4 56 .. 239 300 .. 237 312 .. 0.74 Alignments for each domain: == domain 1 score: 10.2 bits; conditional E-value: 0.00013 EEES-TT-HHHHHH.HHTT-EEEEEEE--TTTHHHHHHH-.........-SEEEES-TTTS- CS DNA_methylase 4 idLfaGiGGfrlgl.eaagfecvaaseidkkaaktYeanfk........kvsigDitkidkk 56 +dL aGiG f+l + ag v a e++++a+ +++n + + ++gD +k++ + tr|F6YP41|F6YP41_MACMU 239 VDLYAGIGYFTLPFlVHAGAAFVHACEWNPHAVVALRNNLEingvadrcQIHFGDNRKLKLS 300 8***********8626788********************98777554444455555544444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (335 nodes) Target sequences: 21211 (10888574 residues searched) Passed MSV filter: 1662 (0.0783556); expected 424.2 (0.02) Passed bias filter: 678 (0.0319645); expected 424.2 (0.02) Passed Vit filter: 63 (0.00297016); expected 21.2 (0.001) Passed Fwd filter: 16 (0.000754326); expected 0.2 (1e-05) Initial search space (Z): 21211 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.49u 0.02s 00:00:00.51 Elapsed: 00:00:00.16 # Mc/sec: 22797.95 // [ok]